[2024-01-25 19:06:20,627] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:06:20,628] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:06:20,628] [INFO] DQC Reference Directory: /var/lib/cwl/stgdb1b9601-395b-48b3-9dd8-aa2766a9aa69/dqc_reference
[2024-01-25 19:06:21,779] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:06:21,780] [INFO] Task started: Prodigal
[2024-01-25 19:06:21,780] [INFO] Running command: gunzip -c /var/lib/cwl/stg52fe74e3-3414-4786-9fe0-9e2b6398e91f/GCF_011297335.1_ASM1129733v1_genomic.fna.gz | prodigal -d GCF_011297335.1_ASM1129733v1_genomic.fna/cds.fna -a GCF_011297335.1_ASM1129733v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:06:42,861] [INFO] Task succeeded: Prodigal
[2024-01-25 19:06:42,862] [INFO] Task started: HMMsearch
[2024-01-25 19:06:42,862] [INFO] Running command: hmmsearch --tblout GCF_011297335.1_ASM1129733v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdb1b9601-395b-48b3-9dd8-aa2766a9aa69/dqc_reference/reference_markers.hmm GCF_011297335.1_ASM1129733v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:06:43,189] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:06:43,190] [INFO] Found 6/6 markers.
[2024-01-25 19:06:43,257] [INFO] Query marker FASTA was written to GCF_011297335.1_ASM1129733v1_genomic.fna/markers.fasta
[2024-01-25 19:06:43,257] [INFO] Task started: Blastn
[2024-01-25 19:06:43,258] [INFO] Running command: blastn -query GCF_011297335.1_ASM1129733v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb1b9601-395b-48b3-9dd8-aa2766a9aa69/dqc_reference/reference_markers.fasta -out GCF_011297335.1_ASM1129733v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:06:44,502] [INFO] Task succeeded: Blastn
[2024-01-25 19:06:44,506] [INFO] Selected 11 target genomes.
[2024-01-25 19:06:44,506] [INFO] Target genome list was writen to GCF_011297335.1_ASM1129733v1_genomic.fna/target_genomes.txt
[2024-01-25 19:06:44,515] [INFO] Task started: fastANI
[2024-01-25 19:06:44,516] [INFO] Running command: fastANI --query /var/lib/cwl/stg52fe74e3-3414-4786-9fe0-9e2b6398e91f/GCF_011297335.1_ASM1129733v1_genomic.fna.gz --refList GCF_011297335.1_ASM1129733v1_genomic.fna/target_genomes.txt --output GCF_011297335.1_ASM1129733v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:07:11,917] [INFO] Task succeeded: fastANI
[2024-01-25 19:07:11,918] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdb1b9601-395b-48b3-9dd8-aa2766a9aa69/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:07:11,918] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdb1b9601-395b-48b3-9dd8-aa2766a9aa69/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:07:11,926] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:07:11,926] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:07:11,927] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Catellatospora methionotrophica	strain=IMSNU 22006	GCA_011297335.1	121620	121620	type	True	100.0	2766	2770	95	conclusive
Catellatospora methionotrophica	strain=NBRC 14553	GCA_016862655.1	121620	121620	type	True	99.9832	2731	2770	95	conclusive
Catellatospora citrea	strain=NBRC 14495	GCA_016862615.1	53366	53366	type	True	90.7635	2100	2770	95	below_threshold
Catellatospora paridis	strain=NEAU-CL2	GCA_009720365.1	1617086	1617086	type	True	90.7093	2133	2770	95	below_threshold
Catellatospora chokoriensis	strain=2-25(1)	GCA_011297315.1	310353	310353	type	True	90.6066	2059	2770	95	below_threshold
Catellatospora vulcania	strain=NEAU-JM1	GCA_009720385.1	1460450	1460450	type	True	90.4275	2202	2770	95	below_threshold
Catellatospora sichuanensis	strain=H14505	GCA_007483665.1	1969805	1969805	type	True	90.2551	2100	2770	95	below_threshold
Phytohabitans suffuscus	strain=NBRC 105367	GCA_011764565.1	624315	624315	type	True	78.2751	1181	2770	95	below_threshold
Actinoplanes ianthinogenes	strain=NBRC 13996	GCA_018324205.1	122358	122358	type	True	77.8145	1113	2770	95	below_threshold
Actinoplanes ianthinogenes	strain=JCM 3249	GCA_014648375.1	122358	122358	type	True	77.8074	1103	2770	95	below_threshold
Cryptosporangium phraense	strain=A-T 5661	GCA_006912135.1	2593070	2593070	type	True	76.4626	778	2770	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:07:11,928] [INFO] DFAST Taxonomy check result was written to GCF_011297335.1_ASM1129733v1_genomic.fna/tc_result.tsv
[2024-01-25 19:07:11,929] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:07:11,929] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:07:11,929] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdb1b9601-395b-48b3-9dd8-aa2766a9aa69/dqc_reference/checkm_data
[2024-01-25 19:07:11,930] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:07:12,005] [INFO] Task started: CheckM
[2024-01-25 19:07:12,006] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011297335.1_ASM1129733v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011297335.1_ASM1129733v1_genomic.fna/checkm_input GCF_011297335.1_ASM1129733v1_genomic.fna/checkm_result
[2024-01-25 19:08:33,274] [INFO] Task succeeded: CheckM
[2024-01-25 19:08:33,275] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:08:33,329] [INFO] ===== Completeness check finished =====
[2024-01-25 19:08:33,329] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:08:33,330] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011297335.1_ASM1129733v1_genomic.fna/markers.fasta)
[2024-01-25 19:08:33,331] [INFO] Task started: Blastn
[2024-01-25 19:08:33,331] [INFO] Running command: blastn -query GCF_011297335.1_ASM1129733v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb1b9601-395b-48b3-9dd8-aa2766a9aa69/dqc_reference/reference_markers_gtdb.fasta -out GCF_011297335.1_ASM1129733v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:08:35,271] [INFO] Task succeeded: Blastn
[2024-01-25 19:08:35,274] [INFO] Selected 11 target genomes.
[2024-01-25 19:08:35,275] [INFO] Target genome list was writen to GCF_011297335.1_ASM1129733v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:08:35,282] [INFO] Task started: fastANI
[2024-01-25 19:08:35,282] [INFO] Running command: fastANI --query /var/lib/cwl/stg52fe74e3-3414-4786-9fe0-9e2b6398e91f/GCF_011297335.1_ASM1129733v1_genomic.fna.gz --refList GCF_011297335.1_ASM1129733v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011297335.1_ASM1129733v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:09:03,253] [INFO] Task succeeded: fastANI
[2024-01-25 19:09:03,261] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:09:03,261] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_011297335.1	s__Catellatospora methionotrophica	100.0	2766	2770	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCF_009720365.1	s__Catellatospora paridis	90.7261	2132	2770	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003610235.1	s__Catellatospora citrea	90.7225	2128	2770	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	97.34	95.99	0.88	0.83	4	-
GCF_009720385.1	s__Catellatospora vulcania	90.4644	2197	2770	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007483665.1	s__Catellatospora sichuanensis	90.2389	2103	2770	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862635.1	s__Catellatospora coxensis	90.1914	2107	2770	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862575.1	s__Catellatospora bangladeshensis	86.5059	1906	2770	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	95.24	95.24	0.85	0.85	2	-
GCF_011764565.1	s__Phytohabitans suffuscus	78.2612	1184	2770	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Phytohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000389965.1	s__Actinoplanes sp000389965	77.8485	981	2770	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018324205.1	s__Actinoplanes ianthinogenes	77.8394	1103	2770	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	99.99	99.99	0.99	0.99	2	-
GCF_006912135.1	s__Cryptosporangium phraense	76.4485	782	2770	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Cryptosporangiaceae;g__Cryptosporangium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:09:03,263] [INFO] GTDB search result was written to GCF_011297335.1_ASM1129733v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:09:03,264] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:09:03,267] [INFO] DFAST_QC result json was written to GCF_011297335.1_ASM1129733v1_genomic.fna/dqc_result.json
[2024-01-25 19:09:03,268] [INFO] DFAST_QC completed!
[2024-01-25 19:09:03,268] [INFO] Total running time: 0h2m43s